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Johnson attended Holmes Chapel Comprehensive School in Cheshire. He began his career as a trainee with Crewe Alexandra, turning professional in 1996. A hard-working midfielder, Johnson's potential led Premier League team Derby County to offer £2.5 million[2] for his signature in 1999. The transfer went through, but Johnson's loyalty to Crewe meant he insisted on staying to help their relegation fight, delaying his move to Derby by two months. In the end, Crewe avoided relegation by a single point.

His continued progress led to a solitary appearance for England, against Italy in November 2000, and further interest in his services. Leeds United ultimately paid £7 million to acquire Johnson on 16 October 2001,[3] but a series of severe injury problems restricted him to just 54 league appearances in four years at Leeds. When Johnson returned to full fitness, Leeds decided not to play him to reduce their liability for transfer fees to Derby.[4] He stayed with the club after their relegation in 2004, and was eventually released in August 2005.

He returned to Derby County in 2005, where he successfully resurrected his career. He played his final game for the club on 28 May 2007 at Wembley Stadium, where he helped the club win the Championship Play-off Final and promotion to the Premier League. However, during the match, Johnson injured his knee, and was substituted with three minutes remaining.[5] He was released from his contract in June 2007, along with seven other players.[6]